Unverified Commit 145fa633 authored by Gaétan Lepage's avatar Gaétan Lepage Committed by GitHub
Browse files

perlPackages.BioExtAlign: bug fix and add test (#380488)

parents 4ef254b3 ebe61cdf

pkgs/by-name/ke/kent/package.nix

+4 −4
Original line number Diff line number Diff line
@@ -53,7 +53,7 @@ stdenv.mkDerivation rec { 
    export HOME=$TMPDIR

    export DESTBINDIR=$HOME/bin



    mkdir -p $HOME/lib $HOME/bin/x86_64

    mkdir -p $HOME/lib $HOME/bin/${stdenv.hostPlatform.parsed.cpu.name}



    cd ./src

    chmod +x ./checkUmask.sh
@@ -63,8 +63,8 @@ stdenv.mkDerivation rec { 
    cd jkOwnLib

    make



    cp ../lib/x86_64/jkOwnLib.a $HOME/lib

    cp ../lib/x86_64/jkweb.a $HOME/lib

    cp ../lib/${stdenv.hostPlatform.parsed.cpu.name}/jkOwnLib.a $HOME/lib

    cp ../lib/${stdenv.hostPlatform.parsed.cpu.name}/jkweb.a $HOME/lib

    cp -r ../inc  $HOME/



    cd ../utils
@@ -79,7 +79,7 @@ stdenv.mkDerivation rec { 
    mkdir -p $out/bin $out/lib $out/inc

    cp $HOME/lib/jkOwnLib.a $out/lib

    cp $HOME/lib/jkweb.a $out/lib

    cp $HOME/bin/x86_64/* $out/bin

    cp $HOME/bin/${stdenv.hostPlatform.parsed.cpu.name}/* $out/bin

    cp -r $HOME/inc/* $out/inc/



    runHook postInstall

pkgs/development/perl-modules/Bio-Ext-Align/default.nix

+19 −5
Original line number Diff line number Diff line
@@ -8,10 +8,7 @@ buildPerlPackage rec { 
  pname = "BioExtAlign";

  version = "1.5.1";



  outputs = [

    "out"

    "dev"

  ];

  outputs = [ "out" ];



  src = fetchFromGitHub {

    owner = "bioperl";
@@ -20,7 +17,15 @@ buildPerlPackage rec { 
    sha256 = "sha256-+0tZ6q3PFem8DWa2vq+njOLmjDvMB0JhD0FGk00lVMA=";

  };



  patches = [ ./fprintf.patch ];

  patches = [

    # Starting for Perl 5.6, implicit function declaration are treated as errors

    # There may be an error but ensembl-vep (the main package for this dependency)

    # runs

    ./no-implicit-function.patch

    # Tests need other parts of BioExt, disabling them

    ./disable-other-tests.patch

    ./fprintf.patch

  ];



  # Do not install other Bio-ext packages

  preConfigure = ''
@@ -32,6 +37,14 @@ buildPerlPackage rec { 
    make

  '';



  checkPhase = ''

    runHook preCheck



    make test



    runHook postCheck

  '';



  meta = {

    homepage = "https://github.com/bioperl/bioperl-ext";

    description = "Write Perl Subroutines in Other Programming Languages";
@@ -39,5 +52,6 @@ buildPerlPackage rec { 
      Part of BioPerl Extensions (BioPerl-Ext) distribution, a collection of Bioperl C-compiled extensions.

    '';

    license = with lib.licenses; [ artistic1 ];

    maintainers = with lib.maintainers; [ apraga ];

  };

}

pkgs/development/perl-modules/Bio-Ext-Align/disable-other-tests.patch

0 → 100644
+84 −0
Original line number Diff line number Diff line 
diff --git a/Bio/Ext/Align/test.pl b/Bio/Ext/Align/test.pl

index 72411f3..1deb77b 100755

--- a/Bio/Ext/Align/test.pl

+++ b/Bio/Ext/Align/test.pl

@@ -8,13 +8,10 @@ my $DEBUG = $ENV{'BIOPERLDEBUG'} || 0;

 BEGIN {

     eval { require Test; };

     use Test;

-    plan tests => 9;

+    plan tests => 4;

 }

 

 use Bio::Ext::Align;

-use Bio::Tools::dpAlign;

-use Bio::Seq;

-use Bio::AlignIO;

 

 $loaded = 1;

 ok(1); # modules loaded

@@ -34,64 +31,3 @@ $alb = &Bio::Ext::Align::Align_Sequences_ProteinSmithWaterman($seq1,$seq2,

 					 $seq2->seq,15,50,STDERR) if $DEBUG;

 

 

-warn( "Testing Local Alignment case...\n") if $DEBUg;

-

-$alnout = new Bio::AlignIO(-format => 'pfam', -fh => \*STDERR);

-$aln = &Bio::Ext::Align::Align_DNA_Sequences("AATGCCATTGACGG",

-					     "CAGCCTCGCTTAG",3,-1,3,1,

-		      Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);

-

-$out = Bio::SimpleAlign->new();

-

-$out->add_seq(Bio::LocatableSeq->new(-seq   => $aln->aln1,

-				     -start => $aln->start1,

-				     -end   => $aln->end1,

-				     -id    => "one"));

-

-$out->add_seq(Bio::LocatableSeq->new(-seq   => $aln->aln2,

-				     -start => $aln->start2,

-				     -end   => $aln->end2,

-				     -id    => "two"));

-$alnout->write_aln($out) if $DEBUG;

-

-$aln = &Bio::Ext::Align::Align_Protein_Sequences("WLGQRNLVSSTGGNLLNVWLKDW","WMGNRNVVNLLNVWFRDW",0,

-						 Bio::Tools::dpAlign::DPALIGN_LOCAL_MILLER_MYERS);

-$out = Bio::SimpleAlign->new();

-ok($aln);

-

-$out->add_seq(Bio::LocatableSeq->new(-seq   => $aln->aln1,

-				     -start => $aln->start1,

-				     -end   => $aln->end1,

-				     -id    => "one"));

-

-$out->add_seq(Bio::LocatableSeq->new(-seq   => $aln->aln2,

-				     -start => $aln->start2,

-				     -end   => $aln->end2,

-				     -id    => "two"));

-$alnout->write_aln($out) if $DEBUG;

-ok(1);

-

-warn( "Testing Global Alignment case...\n") if $DEBUG;

-

-$factory = new Bio::Tools::dpAlign('-alg' => Bio::Tools::dpAlign::DPALIGN_GLOBAL_MILLER_MYERS);

-$s1 = new Bio::Seq(-id => "one", -seq => "AATGCCATTGACGG", -alphabet => 'dna');

-$s2 = new Bio::Seq(-id => "two", -seq => "CAGCCTCGCTTAG", -alphabet => 'dna');

-$aln = $factory->pairwise_alignment($s1, $s2);

-$alnout->write_aln($aln) if $DEBUG;

-$factory->align_and_show($s1, $s2) if $DEBUG;

-

-ok(1);

-

-$s1 = new Bio::Seq(-id => "one", -seq => "WLGQRNLVSSTGGNLLNVWLKDW", 

-		   -alphabet => 'protein');

-$s2 = new Bio::Seq(-id => "two", -seq => "WMGNRNVVNLLNVWFRDW", 

-		   -alphabet => 'protein');

-$aln = $factory->pairwise_alignment($s1, $s2);

-$alnout->write_aln($aln) if $DEBUG;

-$factory->align_and_show($s1, $s2) if $DEBUG;

-ok(1);

-

-$prof = $factory->sequence_profile($s1);

-warn( "Optimal Alignment Score = %d\n", $factory->pairwise_alignment_score($prof, $s2)) if $DEBUG;

-

-ok($factory->pairwise_alignment_score($prof,$s2),77);

pkgs/development/perl-modules/Bio-Ext-Align/fprintf.patch

+1 −1
Original line number Diff line number Diff line
@@ -7,7 +7,7 @@ index 0e07b67..0eab932 100644 
 dpAlign_fatal(char * s)

 {

-    fprintf(stderr, s);

+    fputs(stderr, s);

+    fputs(s, stderr);

     exit(-1);

 }

pkgs/development/perl-modules/Bio-Ext-Align/no-implicit-function.patch

0 → 100644
+13 −0
Original line number Diff line number Diff line 
diff --git a/Bio/Ext/Align/Makefile.PL b/Bio/Ext/Align/Makefile.PL

index cc6c343..ea5cffa 100755

--- a/Bio/Ext/Align/Makefile.PL

+++ b/Bio/Ext/Align/Makefile.PL

@@ -5,7 +5,7 @@ WriteMakefile(

     'NAME'	=> 'Bio::Ext::Align',

     'VERSION'	=> '1.5.1',

     'LIBS'	=> ['-lm'],   # e.g., '-lm' 

-    'DEFINE'	=> '-DPOSIX -DNOERROR',     # e.g., '-DHAVE_SOMETHING' 

+    'DEFINE'	=> '-DPOSIX -DNOERROR -Wno-implicit-function-declaration',     # e.g., '-DHAVE_SOMETHING'

     'INC'	=> '-I./libs',     # e.g., '-I/usr/include/other'

     'MYEXTLIB'  => 'libs/libsw$(LIB_EXT)',

     'clean'     => { 'FILES' => 'libs/*.o libs/*.a' }